Simultaneous nitrite-dependent anaerobic methane and ammonium oxidation processes

Anaerobic oxidation of methane in landfill and adjacent groundwater environments: Occurrence, mechanisms, and potential applications

Landfills remain the predominant means of solid waste management worldwide. Widespread distribution and significant stockpiles of waste in landfills make them a significant source of methane emissions, exacerbating climate change. Anaerobic oxidation of methane (AOM) has been shown to play a critical role in mitigating methane emissions on a global scale. The rich methane and electron acceptor environment in landfills provide the necessary reaction conditions for AOM, making it a potentially low-cost and effective strategy for reducing methane emissions in landfills. However, compared to other anaerobic habitats, research on AOM in landfill environments is scarce, and there is a lack of analysis on the potential application of AOM in different zones of landfills. Therefore, this review summarizes the existing knowledge on AOM and its occurrence in landfills, analyzes the possibility of AOM occurrence in different zones of landfills, discusses its potential applications, and explores the challenges and future research directions for AOM in landfill management. The identification of research gaps and future directions outlined in this review encourages further investigation and advancement in the field of AOM, paving the way for more effective waste stabilization, greenhouse gas reduction, and pollutant mitigation strategies in landfills.

Prospect of denitrifying anaerobic methane oxidation (DAMO) application on wastewater treatment and biogas recycling utilization

Old-fashioned wastewater treatments for nitrogen depend on heterotrophic denitrification process. It would utilize extra organic carbon source as electron donors when the C/N of domestic wastewater was too low to ensure heterotrophic denitrification process. It would lead to non-compliance with carbon reduction targets and impose an economic burden on wastewater treatment. Denitrifying anaerobic methane oxidation (DAMO), which could utilize methane serving as electron donors to replace traditional organic carbon (methanol or sodium acetate), supplies a novel approach for wastewater treatment. As the primary component of biogas, methane is an inexpensive carbon source. With anaerobic digestion becoming increasingly popular for sludge reduction in wastewater treatment plants (WWTPs), efficient biogas utilization through DAMO can offer an environmentally friendly option for in-situ biogas recycling. Here, we reviewed the metabolic principle and relevant research for DAMO and biogas recycling utilization, outlining the prospect of employing DAMO for wastewater treatment and biogas recycling utilization in WWTPs. The application of DAMO provides a new focal point for enhancing efficiency and sustainability in WWTPs.

Revisiting the Engineering Roadmap of Nitrate/Nitrite-Dependent Anaerobic Methane Oxidation

Nitrate/nitrite-dependent anaerobic oxidation of methane (n-DAMO) is a recently discovered process, which provides a sustainable perspective for simultaneous nitrogen removal and greenhouse gas emission (GHG) mitigation by using methane as an electron donor for denitrification. However, the engineering roadmap of the n-DAMO process is still unclear. This work constitutes a state-of-the-art review on the classical and most recently discovered metabolic mechanisms of the n-DAMO process. The versatile combinations of the n-DAMO process with nitrification, nitritation, and partial nitritation for nitrogen removal are also clearly presented and discussed. Additionally, the recent advances in bioreactor development are systematically reviewed and evaluated comprehensively in terms of methane supply, biomass retention, membrane requirement, startup time, reactor performance, and limitations. The key issues including enrichment and operation strategy for the scaling up of n-DAMO-based processes are also critically addressed. Moreover, the challenges inherent to implementing the n-DAMO process in practical applications, including application scenario recognition, GHG emission mitigation, and operation under realistic conditions, are highlighted. Finally, prospects as well as opportunities for future research are proposed. Overall, this review provides a roadmap for potential applications and further development of the n-DAMO process in the field of wastewater treatment.

Enhancement of nitrogen removal in coupling Anammox and DAMO via Fe-modified granular activated carbon

Anaerobic ammonium oxidation (Anammox) coupled with Denitrifying anaerobic methane oxidation (DAMO) is an attractive technology to simultaneously remove nitrogen and mitigate methane emissions from wastewater. However, its nitrogen removal rate is usually limited due to the low methane mass transfer efficiency, low metabolic activity and slow growth rate of functional microorganisms. In this study, GAC and Fe-modified GAC (Fe-GAC) were added into Anammox-DAMO process to investigate their effects on nitrogen removal rates and then reveal the mechanism. The results showed that after 80-day experiments, the total nitrogen removal rate was slightly improved in the presence of GAC (3.94 mg L^-1·d^-1), while it reached high as 16.66 mg L^-1·d^-1 in the presence of Fe-GAC, which was ca.17 times that of non-amended control group (0.96 mg L^-1·d^-1). The addition of Fe-GAC stimulated the secretion of extracellular polymeric substance (EPS), improved the electron transfer capability and promoted the production of Cytochrome C. Besides, the key functional enzyme activities (HZS, HDH and NAR) were highest in the Fe-GAC group, which were approximately 1.06-1.56 times higher than those of GAC-amended and blank control groups. Microbial community analysis showed that the abundance of the DAMO archaea (Candidatus Methanoperedens) and Anammox bacteria (Candidatus Brocadia) were remarkably increased with the addition of Fe-GAC. Functional genes associated with nitrogen removal and methane oxidation in Fe-GAC system were up-regulated. This study provides a promising strategy for achieving high rate of nitrogen removal upon Anammox-DAMO process.

Simultaneous dissolved methane and nitrogen removal from low-strength wastewater using anaerobic granule-based sequencing batch reactor

Anaerobic treatment of mainstream wastewater has been proposed as a promising solution to enhance bioenergy recovery for wastewater treatment plants (WWTPs). However, the limited organics for downstream nitrogen removal and emissions of dissolved methane into the atmosphere are two major barriers to the broad application of anaerobic wastewater treatment. This study aims to develop a novel technology to overcome these two challenges by achieving simultaneous removal of dissolved methane and nitrogen, and unravel the microbial competitions underpinning the process from the microbial and kinetic perspectives. To this end, a laboratory granule-based sequencing batch reactor (GSBR) coupling anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) microorganisms was developed to treat wastewater mimicking effluent from mainstream anaerobic treatment. The GSBR achieved high-level nitrogen and dissolved methane removal rates (> 250 mg N/L/d and > 65 mg CH4/L/d) and efficiencies (> 99% total nitrogen removal and > 90% total methane removal) during the long-term demonstration. The availability of different electron acceptors (nitrite or nitrate) imposed significant effects on the removal of ammonium and dissolved methane, as well as on the microbial communities, and the abundance and expression of functional genes. The analysis of apparent microbial kinetics showed that anammox bacteria had a higher nitrite affinity than n-DAMO bacteria, while n-DAMO bacteria had a higher methane affinity than n-DAMO archaea. These kinetics underpin the observation that nitrite is a preferred electron acceptor for removing ammonium and dissolved methane than nitrate. The findings not only extend the applications of novel n-DAMO microorganisms in nitrogen and dissolved methane removal, but also provide insights into microbial cooperation and competition in granular systems.

Microbial Niche Differentiation during Nitrite-Dependent Anaerobic Methane Oxidation

Nitrite-dependent anaerobic methane oxidation (n-DAMO) has been demonstrated to play important roles in the global methane and nitrogen cycle. However, despite diverse n-DAMO bacteria widely detected in environments, little is known about their physiology for microbial niche differentiation. Here, we show the microbial niche differentiation of n-DAMO bacteria through long-term reactor operations combining genome-centered omics and kinetic analysis. With the same inoculum dominated by both species "Candidatus Methylomirabilis oxyfera" and "Candidatus Methylomirabilis sinica", n-DAMO bacterial population was shifted to "Ca. M. oxyfera" in a reactor fed with low-strength nitrite, but shifted to "Ca. M. sinica" with high-strength nitrite. Metatranscriptomic analysis showed that "Ca. M. oxyfera" harbored more complete function in cell chemotaxis, flagellar assembly, and two-component system for better uptake of nitrite, while "Ca. M. sinica" had a more active ion transport and stress response system, and more redundant function in nitrite reduction to mitigate nitrite inhibition. Importantly, the half-saturation constant of nitrite (0.057 mM vs 0.334 mM NO₂^-) and inhibition thresholds (0.932 mM vs 2.450 mM NO₂^-) for "Ca. M. oxyfera" vs "Ca. M. sinica", respectively, were highly consistent with genomic results. Integrating these findings demonstrated biochemical characteristics, especially the kinetics of nitrite affinity and inhibition determine niche differentiation of n-DAMO bacteria.

Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings

The microbial guild coupling anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is an innovative process to achieve energy-efficient nitrogen removal with the beneficial use of methane in biogas or in anaerobically treated wastewater. Here, metagenomics and metatranscriptomics were used to reveal the microbial ecology of two biofilm systems, which incorporate anammox and n-DAMO for high-level nitrogen removal in low-strength domestic sewage and high-strength sidestream wastewater, respectively. We find that different nitrogen loadings (i.e., 0.1 vs. 1.0 kg N/m3/d) lead to different combinations of anammox bacteria and anaerobic methanotrophs ("Candidatus Methanoperedens" and "Candidatus Methylomirabilis"), which play primary roles for carbon and nitrogen transformations therein. Despite methane being the only exogenous organic carbon supplied, heterotrophic populations (e.g., Verrucomicrobiota and Bacteroidota) co-exist and actively perform partial denitrification or dissimilatory nitrate reduction to ammonium (DNRA), likely using organic intermediates from the breakdown of methane and biomass as carbon sources. More importantly, two novel genomes belonging to "Ca. Methylomirabilis" are recovered, while one surprisingly expresses nitrate reductases, which we designate as "Ca. Methylomirabilis nitratireducens" representing its inferred capability in performing nitrate-dependent anaerobic methane oxidation. This finding not only suggests a previously neglected possibility of "Ca. Methylomirabilis" bacteria in performing methane-dependent nitrate reduction, and also challenges the previous understanding that the methane-dependent complete denitrification from nitrate to dinitrogen gas is carried out by the consortium of bacteria and archaea.

Strategy of nitrate removal in anaerobic ammonia oxidation-dependent processes

The anaerobic ammonium oxidation (anammox), a microbial process that is considered as a low-cost and high efficient wastewater treatment, has received extensive attention with an attractive application prospect. The anammox process reduces nitrite (NO₂^-) to nitrogen gas (N₂) with ammonium (NH₄⁺) as the electron donor. However, some nitrate (NO₃^-) equivalent to 11% of total nitrogen (TN) is generated in this process, which limits the development of anammox. To overcome this problem, many efforts have been made in this regard, mainly combining with other biological treatment methods (denitrification, denitrifying anaerobic methane oxidation, etc.), introducing the substance into anammox process, etc. Herein, we summarized a detailed review of previous researches on the removal of NO₃^- in the anammox-dependent processes. It is hoped that this review could serve as valuable guidance in future research and practical applications of anammox.

Coupling methanotrophic denitrification to anammox in a moving bed biofilm reactor for nitrogen removal under hypoxic conditions

Simultaneous removal of ammonium and nitrate was achieved in a methane-fed moving bed biofilm reactor (MBBR). In the reactor, methanotrophic microorganisms oxidized methane under hypoxic conditions likely to methanol, hence providing an electron donor to denitrifiers to reduce nitrate to nitrite that then allowed anaerobic ammonium oxidizing bacteria (Anammox) to remove excess ammonium as N₂. The ammonium and nitrate removal rates reached 72.09 ± 5.81 mgNH₄⁺-N/L/d and 62.61 ± 4.17 mgNO₃^--N/L/d when the MBBR was operated in continuous mode. Nitrate removal by the methane-fed mixed consortia was confirmed in a batch test revealing a CH₄/NO₃^- molar removal ratio of 1.15. The functional populations were unveiled by FISH analysis and 16S rRNA gene sequencing, which showed that the biofilm was dominated by Anammox bacteria (Candidatus Kuenenia) and diverse taxa associated with the capacity for denitrification: aerobic methanotrophs (Methylobacter, Methylomonas, and unclassified Methylococcaceae), methylotrophic denitrifiers (Opitutaceae and Methylophilaceae), and other heterotrophic denitrifiers (Ignavibacteriaceae, Anaerolineaceae, Comamonadaceae, Rhodocyclaceae and Thauera). Neither DAMO archaea nor DAMO bacteria were found in the sequencing analysis, indicating that more unknown community members possess the metabolic capacity of methanotrophic denitrification.

Rapid enrichment of denitrifying methanotrophs in a series hollow-fiber membrane biofilm reactor

Denitrifying anaerobic methane oxidation (DAMO) process uses methane as electron donor to reduce nitrate/nitrite to dinitrogen, which is a potentially efficient, low-cost and clean biological nitrogen removal technology. However, slow microbial growth rate severely limits the application of this promising process. In this study, a series hollow-fiber membrane biofilm reactor (HfMBR) was operated for 90 days to achieve rapid enrichment of these denitrifying methanotrophs. Finally, the highest relative abundance of denitrifying methanotrophic archaea and bacteria (DAMO archaea and bacteria) reached 47.5% and 11.3%, respectively. And the average abundance of DAMO archaea and bacteria increased 92.9 and 136.6 times respectively during the 90-day enrichment. High growth rate of DAMO archaea with a doubling time of 11.6 days was achieved in the second HfMBR according to quantitative PCR results. The results implied that dissolved oxygen would inhibit the growth of DAMO archaea, but the series HfMBR could effectively counteract this unfavorable factor. This work provided theoretical guidance for the rapid enrichment of denitrifying methanotrophs and contributed to the application of methane-dependent denitrification process.

A mechanistic model for denitrifying anaerobic methane oxidation coupled to dissimilatory nitrate reduction to ammonium

Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) is an important process linking nitrogen and carbon cycle. It is recently demonstrated that n-DAMO archaea are able to couple n-DAMO to dissimilatory nitrate reduction to ammonium (DNRA). In this work, a mathematical model is developed to describe DNRA by n-DAMO archaea for the first time. The anabolic and catabolic processes of n-DAMO archaea, n-DAMO bacteria and anaerobic ammonium oxidation (Anammox) bacteria are involved. The different impacts of exogenous and endogenous nitrite on DNRA and n-DAMO microbes are considered. The developed model is calibrated and validated using experimental data collected from a sequencing batch reactor (SBR) and a counter-diffusion membrane biofilm bioreactor (MBfR). The model outputs fit well with the profiles of nitrogen (N) dynamics and biomass changes in both reactors, demonstrating its good predictive ability. The developed model is further used to simulate the counter-diffusion MBfR incorporating n-DAMO and Anammox process to treat sidestream wastewater. The simulated distribution profiles of N removal/production rates by different microbes along biofilm depth reveal that DNRA by n-DAMO archaea plays an important role in N transformation of the integrated n-DAMO and Anammox process. It is further suggested that the counter-diffusion MBfR under the investigated conditions should be operated at proper hydraulic retention times (HRTs) (i.e. 6h and 8h) with exogenous NO₂^- in the range of 0-10 mg N/L or at HRTs >3h with the absence of exogenous NO₂^- in order to achieve dischargeable effluent.

Efficient nitrogen removal from mainstream wastewater through coupling Partial Nitritation, Anammox and Methane-dependent nitrite/nitrate reduction (PNAM)

The application of partial nitritation and anammox to remove nitrogen from mainstream wastewater is of great interest because of the potential to reduce energy cost and carbon dosage. However, this process confronts a dilemma of relatively high effluent nitrogen concentration (>10 mg N/L), owning to the unwanted prevalence of nitrite-oxidizing bacteria (NOB) and the intrinsic nitrate production by anammox bacteria. Here, a novel technology, named the one-stage PNAM, that integrates Partial Nitritation, Anammox and Methane-dependent nitrite/nitrate reduction reactions, was developed in a single membrane biofilm reactor (MBfR). With feeding of synthetic mainstream wastewater containing ∼50 mg NH₄⁺-N/L at a hydraulic retention time of 12 h, more than 95% nitrogen was removed in the established one-stage PNAM process at a practically useful rate of 0.1 kg N/m³/d. Microbial community characterization and in-situ batch tests revealed a sophisticated microbial structure consisting of ammonia-oxidizing bacteria (AOB), anammox bacteria, nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) bacteria and archaea, and a small fraction of NOB and aerobic methanotrophs. The role of methane in removing nitrate was confirmed by switching on/off the methane supply, which relaxed the requirement for NOB suppression. In addition, the established system was relatively robust against temperature variations, evidenced by a total nitrogen removal efficiency above 80% at temperature as low as 14 ℃. The results provide a promising alternative for efficient nitrogen removal from domestic wastewater using methane as the sole carbon source.

Denitrifying anaerobic methane oxidation (DAMO) cultures: Factors affecting their enrichment, performance and integration with anammox bacteria

The recently discovered process, denitrifying anaerobic methane oxidation (DAMO), links the carbon and nitrogen biogeochemical cycles via coupling the anaerobic oxidation of methane to denitrification. The DAMO process, in this respect, has the potential to mitigate the greenhouse effect through the assimilation of dissolved methane. Denitrification via methane oxidation rather than organic matter, provides a new perspective to performing this once thought to be well established process. The two main species responsible for this process are "Candidatus Methylomirabilis oxyfera (M. oxyfera), and "Candidatus Methanoperedens nitroreducens" (M. nitroreducens). M. oxyfera is responsible of reducing nitrite while M. nitroreducens reduces nitrate to nitrite. These two microorganisms, despite their different pathways, were found to exist together in nature through a syntrophic relationship. Their co-existence with anaerobic ammonium oxidation (Anammox) bacteria was also revealed in the last decade. Anammox bacteria are chemolithoautotrophs, converting ammonium and nitrite to N₂ and nitrate. They are responsible for the release of more than 50% of oceanic N₂, hence play an important role in the global nitrogen cycle. Factors leading to the enrichment of DAMO cultures and their cultivation with Anammox cultures are of significance for improved nitrogen removal systems with decreased greenhouse effect, and even for further full-scale applications. This study, therefore, aims to present an updated review of the DAMO process, by focusing on the factors that might have a significant role in enrichment of DAMO microorganisms and their co-existence with Anammox bacteria. Factors such as temperature, pH, inoculum and feed type, trace metals and reactor configuration are among the ones discussed in detail. Factors, which have not been investigated, are also elucidated to provide a better understanding of the process and set research goals that will aid in the development of DAMO-centered wastewater treatment alternatives.

State-of-the-art management technologies of dissolved methane in anaerobically-treated low-strength wastewaters: A review

The recent advancement in low temperature anaerobic processes shows a great promise for realizing low-energy-cost, sustainable mainstream wastewater treatment. However, the considerable loss of the dissolved methane from anaerobically-treated low-strength wastewater significantly compromises the energy potential of the anaerobic processes and poses an environmental risk. In this review, the promises and challenges of existing and emerging technologies for dissolved methane management are examined: its removal, recovery, and on-site reuse. It begins by describing the working principles of gas-stripping and biological oxidation for methane removal, membrane contactors and vacuum degassers for methane recovery, and on-site biological conversion of dissolved methane into electricity or value-added biochemicals as direct energy sources or energy-compensating substances. A comparative assessment of these technologies in the three categories is presented based on methane treating efficiency, energy-production potential, applicability, and scalability. Finally, current research needs and future perspectives are highlighted to advance the future development of an economically and technically sustainable methane-management technology.

Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications

Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.

Versatility of nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO): First demonstration with real wastewater

Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) processes have been proven effective for nitrogen removal from synthetic wastewater. However, the demonstration using real wastewater has not been achieved yet. To this end, this study investigated the versatile applications of n-DAMO process in real wastewater treatment for the first time. Two methane-based membrane biofilm reactors (MBfRs) were employed to combine anammox and n-DAMO microorganisms, targeting nitrogen removal in mainstream (i.e., domestic sewage) and sidestream (i.e., anaerobic digestion liquor), respectively. Considering various technologies in sewage treatment, three different technical routes, including nitritation + methane-based MBfR, partial nitritation + methane-based MBfR and partial nitritation + anammox + methane-based MBfR, were investigated comprehensively, all producing effluent quality with total nitrogen (TN) at 5 mg N/L or less. Regarding the sidestream treatment, the methane-based MBfR also removed up to 96% TN from the partially nitrified anaerobic digestion liquor at a practically useful rate of 0.5 kg N/m³/d. Microbial communities revealed by 16S rRNA gene amplicon sequencing indicated the dominance of n-DAMO archaea in both reactors, along with the existence of anammox bacteria and n-DAMO bacteria. As the first demonstration of n-DAMO process in real wastewater, this study comprehensively confirmed the applicability of using methane as carbon source to remove nitrogen from both mainstream and sidestream wastewater, supporting their adoption by industries in practice.

Mechanistic Insights into the Dicopper-Complex-Catalyzed Hydroxylation of Methane and Benzene Using Nitric Oxide: A DFT Study

Although hydrocarbons are known to act as reductants for the catalytic reduction of nitric oxides (NO_x) over copper-based catalysts, the reaction mechanism requires clarification. Herein, density functional theory (DFT) calculations were carried out to investigate the reduction mechanisms of NO_x to dinitrogen coupled to the hydroxylation of methane or benzene using the dicopper complex reported by Zhang and co-workers [ J. Am. Chem. Soc. 2019, 141, 10159-10164]. The B3LYP functional was used to optimize the (μ-oxo)(μ-nitrosyl)dicopper complex in the quartet state and the (μ-η²:η²-NO₂)dicopper complex in the doublet state, the latter of which was found to be the ground state. Then, we investigated the reactivities of the (μ-η²:η²-NO₂)dicopper complex toward methane and benzene by considering the conversions of N₂O to N₂ in the presence and the absence of methane or benzene. In the presence of methane and benzene, the calculated activation energies were 27.0 and 21.0 kcal/mol, respectively, whereas that with N₂O alone was prohibitively high (61.9 kcal/mol). Thus, the (μ-η²:η²-NO₂)dicopper complex prefers the reactions with methane and benzene to that with N₂O. The reaction of the (μ-η²:η²-NO₂)dicopper complex with methane or benzene generated the (μ-nitrosyl)dicopper complex. The (μ-nitrosyl)dicopper complex then reacted with N₂O to regenerate the (μ-η²:η²-NO₂)dicopper complex and N₂ with an activation barrier of 31.5 kcal/mol. The overall reactions for methane and benzene hydroxylation were calculated to be exothermic by 41.7 and 54.1 kcal/mol, respectively. These results suggest that the catalytic reduction of NO_x using hydrocarbons is feasible at certain operating temperatures. Thus, our calculations provide new insights into the design of catalysts for NO_x purification.

Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea

Many properties of denitrifying anaerobic methane oxidation (DAMO) bacteria have been explored since their first discovery, while DAMO archaea have attracted less attention. Since nitrate is more abundant than nitrite not only in wastewater but also in the natural environment, in depth investigations of the nitrate-DAMO process should be conducted to determine its environmental significance in the global carbon and nitrogen cycles. This review summarizes the status of research on DAMO archaea and the catalyzed nitrate-dependent anaerobic methane oxidation, including such aspects as laboratory enrichment, environmental distribution, and metabolic mechanism. It is shown that appropriate inocula and enrichment parameters are important for the culture enrichment and thus the subsequent DAMO activity, but there are still relatively few studies on the environmental distribution and physiological metabolism of DAMO archaea. Finally, some hypotheses and directions for future research on DAMO archaea, anaerobic methanotrophic archaea, and even anaerobically metabolizing archaea are also discussed.

Cometabolic removal of organic micropollutants by enriched nitrite-dependent anaerobic methane oxidizing cultures

The innovative and recently discovered n-damo process, based on anaerobic methane oxidation with nitrite, was developed in a membrane-based bioreactor and evaluated in terms of organic micropollutants (OMPs) removal. The main singularity of this study consisted in the evaluation of organic micropollutants (OMPs) removal in the biological reactor. A strategy consisting on progressively increasing the nitrogen loading rate in order to increase the specific denitrification activity was followed to check if the selected OMPs were co-metabolically biotransformed. Significant nitrite removal rate (24.1 mg N L^-1 d^-1) was achieved after only 30 days of operation. A maximum specific removal of 186.3 mg N gVSS^-1 d^-1 was obtained at the end of the operation, which is one of the highest previously reported. A successfully n-damo bacteria enrichment was achieved, being Candidatus Methylomirabilis the predominant bacteria during the whole operation attaining a maximum relative abundance of about 40 %. The natural hormones (E1 and E2) were completely removed in the bioreactor. The specific removal rates of erythromycin (ERY), fluoxetine (FLX), roxithromycin (ROX) and sulfamethoxazole (SMX) were successfully correlated with the specific nitrite removal rates, suggesting a co-metabolic biotransformation.

Learning from microorganisms: using new insights in microbial physiology for sustainable nitrogen management

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To reduce nitrate to N₂ distinct nitrogen-oxide-reducing microorganisms function together.

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Detecting nirS, nirK or narG genes cannot be directly linked to NO and N₂O emission.

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Nitrogen-oxide-reducing specialists can be exploited to reduce NO and N₂O emission from wwtp.

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Aerobic methanotrophs and methane stripping must be considered for the application of N-DAMO.

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Ammonium recovery could be a more sustainable alternative to nitrogen removal.

Diverse nitrogen-transforming microorganisms with a wide variety of physiological properties are employed for biological nitrogen removal from wastewater. There are many technologies that achieve the required nitrogen discharge standards; however, greenhouse gas emissions and energy consumption constitute the bulk of the environmental footprint of wastewater treatment plants. In this review, we highlight current and proposed approaches aiming to achieve more energy-efficient and environment-friendly biological nitrogen removal, discuss whether new discoveries in microbial physiology of nitrogen-transforming microorganisms could be used to reduce greenhouse gas emissions, and summarize recent advances in ammonium recovery from wastewater.

Anaerobic oxidation of methane with denitrification in sediments of a subtropical estuary: Rates, controlling factors and environmental implications

Anaerobic oxidation of methane with denitrification (DAMO), as an important microbial process regulating methane emission, has been widely reported in freshwater ecosystems. However, the DAMO process and associated biogeochemical controls in estuaries remain poorly understood. Here, we used ¹³C- and ¹⁵N-labelling experiments to quantify the potential rates of DAMO and determined the crucial factors controlling the DAMO rates in the sediment of Yangtze Estuary. Potential rates of DAMO varied greatly across the estuary, ranging from 0.07 to 0.28 nmol CO₂ g^-1 d^-1. Salinity negatively affected the DAMO and also showed an indirectly negative influence on DAMO process by high salinity inhibition on NO₃^- availability and denitrification. Nitrate concentrations were significantly correlated with the DAMO rates. Denitrification rates showed positive correlation with DAMO rates, implying that nitrate reduction drives the DAMO process. Sediment total organic carbon and NH₄⁺ had important effects on DAMO rates. These results together indicate that DAMO process can occur and the DAMO rates were mainly controlled by sediment NO₃^- and denitrification in estuary. We further conclude that increasing NO₃^- load can drive the DAMO process with more important implications on methane sink in estuarine ecosystems.

Diversity, enrichment, and genomic potential of anaerobic methane- and ammonium-oxidizing microorganisms from a brewery wastewater treatment plant

Anaerobic wastewater treatment offers several advantages; however, the effluent of anaerobic digesters still contains high levels of ammonium and dissolved methane that need to be removed before these effluents can be discharged to surface waters. The simultaneous anaerobic removal of methane and ammonium by denitrifying (N-damo) methanotrophs in combination with anaerobic ammonium-oxidizing (anammox) bacteria could be a potential solution to this challenge. After a molecular survey of a wastewater plant treating brewery effluent, indicating the presence of both N-damo and anammox bacteria, we started an anaerobic bioreactor with a continuous supply of methane, ammonium, and nitrite to enrich these anaerobic microorganisms. After 14 months of operation, a stable enrichment culture containing two types of 'Candidatus Methylomirabilis oxyfera' bacteria and two strains of 'Ca. Brocadia'-like anammox bacteria was achieved. In this community, anammox bacteria converted 80% of the nitrite with ammonium, while 'Ca. Methylomirabilis' contributed to 20% of the nitrite consumption. The analysis of metagenomic 16S rRNA reads and fluorescence in situ hybridization (FISH) correlated well and showed that, after 14 months, 'Ca. Methylomirabilis' and anammox bacteria constituted approximately 30 and 20% of the total microbial community. In addition, a substantial part (10%) of the community consisted of Phycisphaera-related planctomycetes. Assembly and binning of the metagenomic sequences resulted in high-quality draft genome of two 'Ca. Methylomirabilis' species containing the marker genes pmoCAB, xoxF, and nirS and putative NO dismutase genes. The anammox draft genomes most closely related to 'Ca. Brocadia fulgida' included the marker genes hzsABC, hao, and hdh. Whole-reactor and batch anaerobic activity measurements with methane, ammonium, nitrite, and nitrate revealed an average anaerobic methane oxidation rate of 0.12 mmol h^-1 L^-1 and ammonium oxidation rate of 0.5 mmol h^-1 L^-1. Together, this study describes the enrichment and draft genomes of anaerobic methanotrophs from a brewery wastewater treatment plant, where these organisms together with anammox bacteria can contribute significantly to the removal of methane and ammonium in a more sustainable way. KEY POINTS: • An enrichment culture containing both N-damo and anammox bacteria was obtained. • Simultaneous consumption of ammonia, nitrite, and methane under anoxic conditions. • In-depth metagenomic biodiversity analysis of inoculum and enrichment culture.

Denitrifying Anaerobic Methane Oxidation and Anammox Process in a Membrane Aerated Membrane Bioreactor: Kinetic Evaluation and Optimization

Denitrifying anaerobic methane oxidation (DAMO) coupled to anaerobic ammonium oxidation (anammox) is a promising technology for complete nitrogen removal with economic and environmental benefit. In this work, a model framework integrating DAMO and anammox process was constructed based on suspended-growth systems. The proposed model was calibrated and validated using experimental data from a sequencing batch reactor and a membrane aerated membrane bioreactor (MAMBR). The model managed to describe removal rates of ammonium (NH₄⁺), nitrite (NO₂^-), and total nitrogen, as well as biomass changes of DAMO archaea, DAMO bacteria, and anaerobic ammonium oxidizing bacteria (AnAOB) in both reactors. The estimated parameter values revealed that DAMO archaea possessed properties of faster growth and higher biomass yield in suspended-growth systems compared to those in attached-growth systems (e.g., biofilm). Model simulation demonstrated that solid retention time (SRT) was effective in washing out DAMO bacteria, but retaining DAMO archaea and AnAOB in the MAMBR. The optimal SRT and nitritation efficiency (the ratio of the NO₂^- to the sum of NH₄⁺ and NO₂^- in the MAMBR influent) were simulated so that 99% of total nitrogen was removed to meet the discharge standard. MAMBR further suggested to be operated with SRT between 15 and 30 days so that the optimal nitritation efficiency could be minimized to 49% for cost savings.

Operation strategies of n-DAMO and Anammox process based on microbial interactions for high rate nitrogen removal from landfill leachate

Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) coupling to Anaerobic ammonium oxidation (Anammox) provides an opportunity for simultaneous nitrogen removal and methane emissions mitigation from wastewater. However, to achieve high nitrogen removal rate in such a process remains a critical challenge in practical application. This work investigated the interactions between n-DAMO and Anammox in membrane biofilm reactor (MBfR) and then developed operational strategies of MBfR for high rate nitrogen removal from landfill leachate. Initially, influent containing nitrate and ammonium facilitated the development of n-DAMO and Anammox microorganisms in MBfR, but nitrogen removal performance is hard to be further improved even deteriorated. Detailed investigations of interactions among n-DAMO and Anammox microorganisms confirmed that extra addition of nitrite into MBfR fed with nitrate and ammonium not only stimulated the activities of Anammox bacteria, but also enhanced the activities of n-DAMO archaea from 172.3 to 356.9 mg NO₃^--N L^-1 d^-1. Functional gene analysis also indicated that mcrA and hzsA genes increased after nitrite addition. Based on this finding, influent containing NO₃^-, NO₂^- and NH₄⁺ enabled nitrogen removal rates of MBfR increase from 224.9 to 888.2 mg N L^-1 d^-1. Finally, nitrate in the influent was gradually replaced with nitrite to mimic the effluent from partial nitriation of landfill leachate, but maintain the nitrate availability for n-DAMO archaea through increasing nitrate production from Anammox. These operation strategies enabled MBfR achieve the steady state with a nitrogen removal rate of 6.1 kg N m^-3 d^-1. Microbial community analysis revealed n-DAMO archaea, n-DAMO bacteria and Anammox bacteria jointly dominated the biofilm, and their relative abundance dynamically shifted with feeding regime. This work provides promising operational strategies for high rate of nitrogen removal from landfill leachate through integrating n-DAMO and Anammox process.

New perspectives on microbial communities and biological nitrogen removal processes in wastewater treatment systems

Biological nitrogen removal (BNR) is a critical process in wastewater treatment. Recently, there have new microbial communities been discovered to be capable of performing BNR with novel metabolic pathways. This review presents the up-to-date status on these microorganisms, including ammonia oxidizing archaea (AOA), complete ammonia oxidation (COMAMMOX) bacteria, anaerobic ammonium oxidation coupled to iron reduction (FEAMMOX) bacteria, anaerobic ammonium oxidation (ANAMMOX) bacteria and denitrifying anaerobic methane oxidation (DAMO) microorganism. Their metabolic pathways and enzymatic reactions in nitrogen cycle are demonstrated. Generally, these novel microbial communities have advantages over canonical nitrifiers or denitrifiers, such as higher substrate affinities, better physicochemical tolerances and/or less greenhouse gas emission. Also, their recent development and/or implementation in BNR is discussed and outlook. Finally, the key implications of coupling these microbial communities for BNR are identified. Overall, this review illustrates novel microbial communities that could provide new possibilities for high-performance and energy-saving nitrogen removal from wastewater.

Nitrogen loss by anaerobic ammonium oxidation in a mangrove wetland of the Zhangjiang Estuary, China

Anaerobic ammonium oxidation (anammox), a microbial process in which NH₄⁺ is oxidized to N₂ gas, is considered a significant nitrogen cycle process, but its significance in mangrove wetland sediments, particularly its depth- and genus-specific distribution and activity have remained uncertain. Here we report the vertical distribution, abundance, activity and role of anammox bacteria in mangrove sediments of Zhangjiang Estuary, China. We used stable isotope-tracer techniques, 16S rRNA and anammox bacterial functional gene (Hydrazine synthase B: hzsB) clone libraries and quantitative polymerase chain reaction (qPCR) assays, along with an assessment of nutrient profiles of sediment core samples. We observed a widespread occurrence of anammox bacteria at different depths of mangrove sediments. The abundance of anammox bacterial 16S rRNA and hzsB genes ranged from 0.41×10⁷ to 9.74×10⁷ and from 0.42×10⁶ to 6.44×10⁶ copies per gram of dry soil and peaked in the upper layer of mangrove sediments. We also verified the co-occurrence of different genera of anammox microorganisms in mangrove sediments, with Candidatus Scalindua and Candidatus Kuenenia being the dominant genera. Potential anammox rates ranged from 4.83 to 277.36 nmolN₂·g^-1·d^-1 at different depths of sediment cores, and the highest rates were found in the deeper layer (70-100cm) of mangrove sediments. Scaling our findings up to the entire mangrove system, we estimated that anammox hotspots accounted for a loss of 751 gN·m^-2·y^-1, and contributed to over 12% of the nitrogen lost from the deeper layer of mangrove sediments in this region.

Methane emissions from aqueous sediments are influenced by complex interactions among microbes and environmental factors: A modeling study

Methane fluxes from aqueous sediments strongly influence global atmospheric methane. However, many questions still puzzle researchers; for example, why are some unstable sediments atmospheric methane sinks? In this study, a biofilm model originally developed for wastewater treatment was modified to simulate the microbial kinetics and substance conversions in aqueous surface sediments. The model was validated by the experimental data and could predict chemical profiles and microbial distributions in sediments. The model revealed complicated interactions between different microbial communities and environmental factors, including competition between aerobic methane-oxidizing bacteria, nitrite-dependent anaerobic methane-oxidizing bacteria, and anaerobic ammonia-oxidizing bacteria. The results of model simulations showed that the effects of environmental factors, especially dissolved oxygen and ammonia in overlying water, on methane fluxes are very complicated. Rapid environmental changes (which can be caused by tide, day-night alternation, or zoobenthic and human activity) and intensive competition between microbes greatly affected methane fluxes and resulted in alternation between atmospheric methane source and sink in unstable sediments. This study extends the application of a wastewater treatment model to ecological studies of microbial interactions in natural sediments and explains some problems that might be difficult to resolve by using experimental methods.

High-level nitrogen removal by simultaneous partial nitritation, anammox and nitrite/nitrate-dependent anaerobic methane oxidation

While the anaerobic ammonium oxidation (anammox) process has been applied for nitrogen removal from high-strength wastewater, nitrate accumulation in effluent still represents a major concern. Here, a novel process, named the one-stage PNAM, that integrates the Partial Nitritation (PN), Anammox and Methane-dependent nitrite/nitrate reduction reactions in a single membrane biofilm reactor (MBfR) is developed. With feeding of 1030 mg NH4+-N/L at a hydraulic retention time of 16 h, the proposed one-stage PNAM process achieved an average total nitrogen removal efficiency of 98% and a nitrogen removal rate of 1.5 kg N/m3/d (1.4-1.8 g N/m2/d) by using methane as the sole carbon-based electron donor. The N2O emission was determined to be 0.34% ± 0.01%. Microbial community characterization revealed that ammonia-oxidizing bacteria (AOB), anammox bacteria, nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) bacteria and archaea co-developed in the biofilm. Batch tests showed that AOB, anammox bacteria and n-DAMO microorganisms were indeed jointly responsible for the nitrogen removal. This one-stage PNAM process can potentially be applied to treating high-strength wastewater, such as anaerobic sludge digestion liquor or landfill leachate.

Reducing Cost and Environmental Impact of Wastewater Treatment with Denitrifying Methanotrophs, Anammox, and Mainstream Anaerobic Treatment

In water resource recovery facilities, sidestream biological nitrogen removal via anaerobic ammonium oxidation (anammox) is more energy and cost efficient than conventional nitrification-denitrification. However, under mainstream conditions, nitrite oxidizing bacteria (NOB) out-select anammox bacteria for nitrite produced by ammonium oxidizing bacteria (AOB). Therefore, nitrite production is the bottleneck in mainstream anammox nitrogen removal. Nitrate-dependent denitrifying anaerobic methane oxidizing archaea (n-damo) oxidize methane and reduce nitrate to nitrite. The nitrite supply challenge in mainstream anammox implementation could be solved with a microbial community of AOB, NOB, n-damo, and anammox with methane from anaerobic sludge digestion or a mainstream anaerobic membrane bioreactor (AnMBR). The cost and environmental impact of traditional nitrification/dentrification relative to AOB/anammox and AOB/anammox/n-damo systems, with and without an AnMBR, were compared with a stoichiometric model. AnMBR implementation reduced costs and emission rates at moderate to high nutrient loading by lowering aeration and sludge handling demands while increasing methane available for cogeneration. AnMBR/AOB/anammox systems reduced cost and GHG emission by up to $0.303/d/m³ and 1.72 kg equiv. CO₂/d/m³, respectively, while AnMBR/AOB/anammox/n-damo systems saw a similar reduction of at least $0.300/d/m³ and 1.65 kg equiv. CO₂/d/m³ in addition to alleviating the necessity to stop nitrification at nitrate, allowing easier aeration control.

Achieving high nitrogen removal efficiency by optimizing nitrite-dependent anaerobic methane oxidation process with growth factors

Nitrite-dependent anaerobic methane oxidation (N-DAMO) is a newly discovered bioprocess which uses methane as electron donor to reduce nitrite into dinitrogen. It is a promising clean bioprocess for denitrification in wastewater treatment. However, the low reaction rate and slow growth rate of N-DAMO bacteria within NC10 phylum limit the application of the process. In this study, we chose vitamin, heme, nucleobase and betaine to investigate their short- and long-term effects on N-DAMO bacteria. The concentrations of the growth factors of medium were improved according to the short-term experiments. The results were subsequently verified via long-term inoculations and were applied in a magnetically stirred gas lift reactor (MSGLR). The results indicated that nucleobase and betaine (5.0 and 200 μg L^-1, respectively) significantly stimulated the N-DAMO activity, whereas vitamin and heme had no significant effects in the tested concentration ranges. During the long-term incubation, N-DAMO bacteria continuously increased and finally achieved a relative abundance of 14.4% on day 300. Notably, larger aggregates of N-DAMO bacteria were observed at the end of the long-term incubation. And the nitrogen removal rate of the MSGLR increased to 70 mg N L^-1 day^-1, with the total nitrogen removal efficiency over 99.0%. However, the addition of betaine introduced methyl into the reactors and this made methylotrophs account a considerable part of the bacterial community, which limited the enrichment degree of N-DAMO bacteria. This work will contribute to the engineering application and enrichment of N-DAMO bacteria.

Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers

Oxygenic denitrification represents a new route in reductive nitrogen turnover which differs from canonical denitrification in how nitric oxide (NO) is transformed into dinitrogen gas. Instead of NO reduction via N₂O to N₂, NO is proposed to be directly disproportionated into N₂ and O₂ in oxygenic denitrification, catalyzed by the putative NO dismutase (Nod). Although a high diversity of nod genes has been recovered from various environments, still little is known about the niche partitioning and ecophysiology of oxygenic denitrifiers. One constraint is that nod as a functional marker for oxygenic denitrifiers is not well established. To address this issue, we compared the diversity and phylogeny of nod, 16S rRNA and pmoA gene sequences of four NC10 enrichments that are capable of methane-driven oxygenic denitrification and one environmental sample. The phylogenies of nod, 16S rRNA and pmoA genes of these cultures were generally congruent. The diversity of NC10 bacteria inferred from different genes was also similar in each sample. A new set of NC10-specific nod primers was developed and used in qPCR. The abundance of NC10 bacteria inferred from nod genes was constantly lower than via 16S rRNA genes, but the difference was within one order of magnitude. These results suggest that nod is a suitable molecular marker for studying the diversity and phylogeny of methane-driven oxygenic denitrifiers, the further investigation of which may be of value to develop enhanced strategies for sustainable nitrogen or methane removal.

Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges

Functional differentiation and metabolite exchange enable microbial consortia to perform complex metabolic tasks and efficiently cycle the nutrients. Inspired by the cooperative relationships in environmental microbial consortia, synthetic microbial consortia have great promise for studying the microbial interactions in nature and more importantly for various engineering applications. However, challenges coexist with promises, and the potential of consortium-based technologies is far from being fully harnessed. Thorough understanding of the underlying molecular mechanisms of microbial interactions is greatly needed for the rational design and optimization of defined consortia. These knowledge gaps could be potentially filled with the assistance of the ongoing revolution in systems biology and synthetic biology tools. As current fundamental and technical obstacles down the road being removed, we would expect new avenues with synthetic microbial consortia playing important roles in biological and environmental engineering processes such as bioproduction of desired chemicals and fuels, as well as biodegradation of persistent contaminants.

Interactions between anaerobic ammonium- and methane-oxidizing microorganisms in a laboratory-scale sequencing batch reactor

The reject water of anaerobic digestors still contains high levels of methane and ammonium that need to be treated before these effluents can be discharged to surface waters. Simultaneous anaerobic methane and ammonium oxidation performed by nitrate/nitrite-dependent anaerobic methane-oxidizing(N-damo) microorganisms and anaerobic ammonium-oxidizing(anammox) bacteria is considered a potential solution to this challenge. Here, a stable coculture of N-damo archaea, N-damo bacteria, and anammox bacteria was obtained in a sequencing batch reactor fed with methane, ammonium, and nitrite. Nitrite and ammonium removal rates of up to 455 mg N-NO₂^- L^-1 day^-1 and 228 mg N-NH₄⁺ L^-1 were reached. All nitrate produced by anammox bacteria (57 mg N-NO₃^- L^-1 day^-1) was consumed, leading to a nitrogen removal efficiency of 97.5%. In the nitrite and ammonium limited state, N-damo and anammox bacteria each constituted about 30-40% of the culture and were separated as granules and flocs in later stages of the reactor operation. The N-damo archaea increased up to 20% and mainly resided in the granular biomass with their N-damo bacterial counterparts. About 70% of the nitrite in the reactor was removed via the anammox process, and batch assays confirmed that anammox activity in the reactor was close to its maximal potential activity. In contrast, activity of N-damo bacteria was much higher in batch, indicating that these bacteria were performing suboptimally in the sequencing batch reactor, and would probably be outcompeted by anammox bacteria if ammonium was supplied in excess. Together these results indicate that the combination of N-damo and anammox can be implemented for the removal of methane at the expense of nitrite and nitrate in future wastewater treatment systems.

Rates and pathways of CH4 oxidation in ferruginous Lake Matano, Indonesia

This study evaluates rates and pathways of methane (CH₄ ) oxidation and uptake using ¹⁴ C-based tracer experiments throughout the oxic and anoxic waters of ferruginous Lake Matano. Methane oxidation rates in Lake Matano are moderate (0.36 nmol L^-1  day^-1 to 117 μmol L^-1  day^-1 ) compared to other lakes, but are sufficiently high to preclude strong CH₄ fluxes to the atmosphere. In addition to aerobic CH₄ oxidation, which takes place in Lake Matano's oxic mixolimnion, we also detected CH₄ oxidation in Lake Matano's anoxic ferruginous waters. Here, CH₄ oxidation proceeds in the apparent absence of oxygen (O₂ ) and instead appears to be coupled to some as yet uncertain combination of nitrate ( NO 3 - ), nitrite ( NO 2 - ), iron (Fe) or manganese (Mn), or sulfate ( SO 4 2 - ) reduction. Throughout the lake, the fraction of CH₄ carbon that is assimilated vs. oxidized to carbon dioxide (CO₂ ) is high (up to 93%), indicating extensive CH₄ conversion to biomass and underscoring the importance of CH₄ as a carbon and energy source in Lake Matano and potentially other ferruginous or low productivity environments.

Key Physiology of a Nitrite-Dependent Methane-Oxidizing Enrichment Culture

Nitrite-dependent methane-oxidizing bacteria couple the reduction of nitrite to the oxidation of methane via a unique oxygen-producing pathway. This process is carried out by members of the genus Methylomirabilis that belong to the NC10 phylum. Contrary to other known anaerobic methane oxidizers, they do not employ the reverse methanogenesis pathway for methane activation but instead a canonical particulate methane monooxygenase similar to those used by aerobic methanotrophs. Methylomirabilis-like bacteria are detected in many natural and manmade ecosystems, but their physiology is not well understood. Here, using continuous cultivation techniques, batch activity assays, and state-of-the-art membrane-inlet mass spectrometry, we determined growth rate, doubling time, and methane and nitrite affinities of the nitrite-dependent methane-oxidizing bacterium "Candidatus Methylomirabilis lanthanidiphila." Our results provide insight into understanding the interactions of these microorganisms with methanotrophs and other nitrite-reducing microorganisms, such as anaerobic ammonium-oxidizing bacteria. Furthermore, our data can be used in modeling studies as well as wastewater treatment plant design.IMPORTANCE Methane is an important greenhouse gas with a radiative forcing 28 times that of carbon dioxide over a 100-year time scale. The emission of methane to the atmosphere is controlled by aerobic and anaerobic methanotrophs, which are microorganisms that are able to oxidize methane to conserve energy. While aerobic methanotrophs have been studied for over a century, knowledge on the physiological characteristics of anaerobic methanotrophs is scarce. Here, we describe kinetic properties of "Candidatus Methylomirabilis lanthanidiphila," a nitrite-dependent methane-oxidizing microorganism, which is ecologically important and can be applied in wastewater treatment.

Enhancing mainstream nitrogen removal by employing nitrate/nitrite-dependent anaerobic methane oxidation processes

Due to serious eutrophication in water bodies, nitrogen removal has become a critical stage for wastewater treatment plants (WWTPs) over past decades. Conventional biological nitrogen removal processes are based on nitrification and denitrification (N/DN), and are suffering from several major drawbacks, including substantial aeration consumption, high fugitive greenhouse gas emissions, a requirement for external carbon sources, excessive sludge production and low energy recovery efficiency, and thus unable to satisfy the escalating public needs. Recently, the discovery of anaerobic ammonium oxidation (anammox) bacteria has promoted an update of conventional N/DN-based processes to autotrophic nitrogen removal. However, the application of anammox to treat domestic wastewater has been hindered mainly by unsatisfactory effluent quality with nitrogen removal efficiency below 80%. The discovery of nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) during the last decade has provided new opportunities to remove this barrier and to achieve a robust system with high-level nitrogen removal from municipal wastewater, by utilizing methane as an alternative carbon source. In the present review, opportunities and challenges for nitrate/nitrite-dependent anaerobic methane oxidation are discussed. Particularly, the prospective technologies driven by the cooperation of anammox and n-DAMO microorganisms are put forward based on previous experimental and modeling studies. Finally, a novel WWTP system acting as an energy exporter is delineated.

Salinity stress changed the biogeochemical controls on CH4 and N2O emissions of estuarine and intertidal sediments

Elevated salinity is expected to drive changes in biogeochemical cycling and microbial communities in estuarine and intertidal wetlands. However, limited information regarding the role of salinity in shaping biogeochemical controls and mediating greenhouse gas emissions is currently available. In this study, we used incubation experiment across salinity gradients of the estuarine and intertidal sediments to reveal the underlying interconnections of CH₄ and N₂O emissions, biogeochemical controls and salinity gradients. Our results indicated that sediment biogeochemical properties were significantly affected by the increasing salinity, which were attributed to the accelerated sediment enzyme activities. The increasing salinity promoted CH₄ and N₂O emission rates by stimulating organic carbon decomposition and nitrogen transformation rates. In addition, the copy number of mcrA, nirS and nirK genes increased along with the salinity gradients, which strongly mediated the CH₄ and N₂O emission rates. Stepwise regression analysis suggested that labile organic carbon and denitrification were the most crucial determinants of CH₄ and N₂O emission rates, respectively. Overall, salinity could enhance CH₄ and N₂O emission mainly by altering sediment geochemical variables, microbial activity and functional gene abundance in estuarine and intertidal environments. Furthermore, increasing salinity could enhance the carbon and nitrogen export, which may pose a threat to the ecological function of estuarine and intertidal ecosystems. This study may contribute to the knowledge about the importance of biogeochemical controls induced by salinity in mediating greenhouse gas emissions.

Response of the Anaerobic Methanotroph "Candidatus Methanoperedens nitroreducens" to Oxygen Stress

"Candidatus Methanoperedens nitroreducens" is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In natural and man-made ecosystems, this archaeon is often found at oxic-anoxic interfaces where nitrate, the product of aerobic nitrification, cooccurs with methane produced by methanogens. As such, populations of "Ca Methanoperedens nitroreducens" could be prone to regular oxygen exposure. Here, we investigated the effect of 5% (vol/vol) oxygen exposure in batch activity assays on a "Ca Methanoperedens nitroreducens" culture, enriched from an Italian paddy field. Metagenome sequencing of the DNA extracted from the enrichment culture revealed that 83% of 16S rRNA gene reads were assigned to a novel strain, "Candidatus Methanoperedens nitroreducens Verserenetto." RNA was extracted, and metatranscriptome sequencing upon oxygen exposure revealed that the active community changed, most notably in the appearance of aerobic methanotrophs. The gene expression of "Ca Methanoperedens nitroreducens" revealed that the key genes encoding enzymes of the methane oxidation and nitrate reduction pathways were downregulated. In contrast to this, we identified upregulation of glutaredoxin, thioredoxin family/like proteins, rubrerythrins, peroxiredoxins, peroxidase, alkyl hydroperoxidase, type A flavoproteins, FeS cluster assembly protein, and cysteine desulfurases, indicating the genomic potential of "Ca Methanoperedens nitroreducens Verserenetto" to counteract the oxidative damage and adapt in environments where they might be exposed to regular oxygen intrusion.IMPORTANCE "Candidatus Methanoperedens nitroreducens" is an anaerobic archaeon which couples the reduction of nitrate to the oxidation of methane. This microorganism is present in a wide range of aquatic environments and man-made ecosystems, such as paddy fields and wastewater treatment systems. In such environments, these archaea may experience regular oxygen exposure. However, "Ca Methanoperedens nitroreducens" is able to thrive under such conditions and could be applied for the simultaneous removal of dissolved methane and nitrogenous pollutants in oxygen-limited systems. To understand what machinery "Ca Methanoperedens nitroreducens" possesses to counteract the oxidative stress and survive, we characterized the response to oxygen exposure using a multi-omics approach.

Optimization of methane-dependent oxygenic denitrification in sequencing batch reactors by insights into the microbial interactions

Methane-dependent oxygenic denitrification (O2DN) is a promising technology used for reducing greenhouse gas emissions of nitrous oxide (N₂O) during wastewater treatment. Heterotrophic bacteria are associated with methane-dependent O2DN bacteria, and it has been proposed that metabolic cross-feeding occurs between the two populations above. In this study, a mathematical model was developed to describe the microbial processes and interactions between methane-dependent O2DN bacteria and associated heterotrophic bacteria in a sequencing batch reactor (SBR). A growth factor-dependent decoupling of metabolism and growth of methane-dependent O2DN bacteria was introduced into the model. Effects of influent substrates, operating parameters, and initial biomass on microbial community and reactor performance were then investigated, and the above parameters were optimized using the model. Results surprisingly show that organic matter in the influent greatly stimulated the growth of methane-dependent O2DN bacteria but slightly limited the increase of heterotrophic bacteria. This effect could be explained by the increased excretion of growth factors by heterotrophic bacteria and the intensified competition for nitrite when methane-dependent O2DN bacteria increased. These results will assist in providing a new understanding of microbial interactions in methane-dependent O2DN systems and offer a new and efficient strategy for operating methane-dependent O2DN reactors.

Effect of methane partial pressure on the performance of a membrane biofilm reactor coupling methane-dependent denitrification and anammox

Complete nitrogen removal has recently been demonstrated by integrating anaerobic ammonium oxidation (anammox) and denitrifying anaerobic methane oxidation (DAMO) processes. In this work, the effect of methane partial pressure on the performance of a membrane biofilm reactor (MBfR) consisting of DAMO and anammox microorganisms was evaluated. The activities of DAMO archaea and DAMO bacteria in the biofilm increased significantly with increased methane partial pressure, from 367 ± 9 and 58 ± 22 mg-N L^-1d^-1 to 580 ± 12 and 222 ± 22 mg-N L^-1d^-1, respectively, while the activity of anammox bacteria only increased slightly, when the methane partial pressure was elevated from 0.24 to 1.39 atm in the short-term batch tests. The results were supported by a long-term (seven weeks) continuous test, when the methane partial pressure was dropped from 1.39 to 0.78 atm. The methane utilization efficiency was always above 96% during both short-term and long-term tests. Taken together, nitrogen removal rate (especially the nitrate reduction rate by DAMO archaea) and methane utilization efficiency could be maintained at high levels in a broad range of methane partial pressure (0.24-1.39 atm in this study). In addition, a previously established DAMO/anammox biofilm model was used to analyze the experimental data. The observed impacts of methane partial pressure on biofilm activity were well explained by the modeling results. These results suggest that methane partial pressure can potentially be used as a manipulated variable to control reaction rates, ultimately to maintain high nitrogen removal efficiency, according to nitrogen loading rate.

Bloom of a denitrifying methanotroph, 'Candidatus Methylomirabilis limnetica', in a deep stratified lake

Methanotrophic bacteria represent an important biological filter regulating methane emissions into the atmosphere. Planktonic methanotrophic communities in freshwater lakes are typically dominated by aerobic gamma-proteobacteria, with a contribution from alpha-proteobacterial methanotrophs and the NC10 bacteria. The NC10 clade encompasses methanotrophs related to 'Candidatus Methylomirabilis oxyfera', which oxidize methane using a unique pathway of denitrification that tentatively produces N₂ and O₂ from nitric oxide (NO). Here, we describe a new species of the NC10 clade, 'Ca. Methylomirabilis limnetica', which dominated the planktonic microbial community in the anoxic depths of the deep stratified Lake Zug in two consecutive years, comprising up to 27% of the total bacterial population. Gene transcripts assigned to 'Ca. M. limnetica' constituted up to one third of all metatranscriptomic sequences in situ. The reconstructed genome encoded a complete pathway for methane oxidation, and an incomplete denitrification pathway, including two putative nitric oxide dismutase genes. The genome of 'Ca. M. limnetica' exhibited features possibly related to genome streamlining (i.e. less redundancy of key metabolic genes) and adaptation to its planktonic habitat (i.e. gas vesicle genes). We speculate that 'Ca. M. limnetica' temporarily bloomed in the lake during non-steady-state conditions suggesting a niche for NC10 bacteria in the lacustrine methane and nitrogen cycle.

Integration of methane removal in aerobic anammox-based granular sludge reactors

Combined partial nitritation-anaerobic ammonium oxidation (anammox) processes have been widely applied for nitrogen removal from anaerobic digestion reject water. However, such streams also contain dissolved methane that can escape to the atmosphere, hence contributing to global warming. This study investigates the possibility of integrating methane removal in aerobic anammox-based granular sludge reactors, through modelling and simulation. Methane removal could be established through aerobic methane-oxidizing bacteria (MOB), denitrifying anaerobic methane-oxidizing bacteria (damoB, NO₂^- + CH₄ → N₂ + CO₂), and/or archaea (damoA, NO₃^- + CH₄ → NO₂^- + CO₂). The simulation results demonstrated that the combined removal of nitrogen and methane was feasible at low dissolved oxygen conditions. Aerobic MOB were the main responsible microorganisms for removing methane. A sensitivity analysis of key kinetic parameters showed a shift in the methanotrophic populations depending on the most favourable parameters for each microbial group, while keeping high nitrogen and methane removal efficiencies. Possible methane stripping during aeration could be limited by increasing the depth within the reactor column at which aeration was supplied. Overall, the integration of methane removal in aerobic anammox-based granular sludge reactors seems to be a promising process option to reduce the carbon footprint from wastewater treatment.

The content of trace element iron is a key factor for competition between anaerobic ammonium oxidation and methane-dependent denitrification processes

Coupling of anaerobic ammonium oxidation (Anammox) with denitrifying anaerobic methane oxidation (DAMO) is a sustainable pathway for nitrogen removal and reducing methane emissions from wastewater treatment processes. However, studies on the competitive relation between Anammox bacteria and DAMO bacteria are limited. Here, we investigated the effects of variations in the contents of trace element iron on Anammox and DAMO microorganisms. The short-term results indicated that optimal concentrations of iron, which obviously stimulated the activity of Amammox bacteria, DAMO bacteria and DAMO archaea, were 80, 20, and 80 μM, respectively. The activity of Amammox bacteria increased more significant than DAMO bacteria with increasing contents of trace element iron. After long-term incubation with high content of trace element iron of 160 μM in the medium, Candidatus Brocadia (Amammox bacteria) outcompeted Candidatus Methylomirabilis oxyfera (DAMO bacteria), and ANME-2d (DAMO archaea) remarkably increased in number and dominated the co-culture systems (64.5%). Meanwhile, with further addition of iron, the removal rate of ammonium and nitrate increased by 13.6 and 9.2 times, respectively, when compared with that noted in the control. As far as we know, this study is the first to explore the important role of trace element iron contents in the competition between Anammox bacteria and DAMO bacteria and further enrichment of DAMO archaea by regulating the contents of trace element iron.

Oxygenic denitrification for nitrogen removal with less greenhouse gas emissions: Microbiology and potential applications

Nitrogen pollution is a worldwide problem and has been extensively treated by canonical denitrification (CDN) process. However, the CDN process generates several issues such as intensive greenhouse gas (GHG) emissions. In the past years, a novel biological nitrogen removal (BNR) process of oxygenic denitrification (O2DN) has been proposed as a promising alternative to the CDN process. The classic denitrification four steps are simplified to three steps by O2DN bacteria without producing and releasing the intermediate nitrous oxide (N₂O), a potent GHG. In this article, we summarized the findings in previous literatures as well as our results, including involved microorganisms and metabolic mechanisms, functional genes and microbial detection, kinetics and influencing factors and their potential applications in wastewater treatment. Based on our knowledge and experience, the benefits and limitations of the current O2DN process were analyzed. Since O2DN is a new field in wastewater treatment, more research and application is required, especially the development of integrated processes and the quantitative assessment of the contribution of O2DN process in natural habitats and engineered systems.

Microbial pathways for nitrogen loss in an upland soil

The distribution and importance of anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) have been identified in aquatic ecosystems; their role in agricultural upland soils however has not yet been well investigated. In this study, we examined spatio-temporal distributions of anammox and n-damo bacteria in soil profiles (300 cm depth) from an agricultural upland. Monitoring nitrogen (N) conversion activity using isotope-tracing techniques over the course of one year showed denitrification (99.0% N-loss in the winter and 85.0% N-loss in the summer) predominated over anammox (1.0% N-loss in the winter and 14.4% N-loss in the summer) and n-damo (0.6% N-loss in the winter) in surface soils (0-20 cm). While below 20 cm depth, N-loss was dominated by anammox (79.4 ± 14.3% in the winter and 65.4 ± 12.5% in the summer) and n-damo was not detected. Phylogenetic analysis showed that Candidatus Brocadia anammoxidans dominated the anammox community in the surface soil and Candidatus Brocadia fulgida dominated below 20 cm depth. Dissimilatory nitrate reduction to ammonium (DNRA), another nitrite reduction process, was found to play a limited role (4.9 ± 3.5%) in the surface soil compared with denitrification; below 80 cm DNRA rates were much higher than rates of anammox and denitrification. Ammonium oxidation was the main source of NO2- above 80 cm (70.9 ± 23.3%), the key influencing factor on anammox rates, and nitrate reduction (100%) was the main NO2- source below 80 cm. Considering the anammox, n-damo and denitrification rates as a whole in the sampled soil profile, denitrification is still the main N-loss process in upland soils.

Current perspectives on the application of N-damo and anammox in wastewater treatment

The efficient treatment of wastewater for the removal of nitrogen is of key importance to prevent eutrophication and deoxygenation of receiving water bodies. In addition, ineffective wastewater treatment can be a source of greenhouse gasses. The application of newly discovered microbial processes, such as nitrite/nitrate-dependent methane oxidation (N-damo), can make wastewater treatment systems more sustainable; especially when they are combined with anaerobic ammonium oxidation (anammox). A treatment system based on these microbial processes will need oxygen supply for the production of nitrite. This oxygen may inhibit N-damo and anammox and careful regulation of the oxygen supply is of key importance for the success of the application of N-damo in wastewater treatment.